Glossary

Allele - one of several different
forms of a gene at a particular place
on a chromosome. Alleles are located
on opposite pairs of chromosomes, but in the same relative place.

Amino Acid - The building blocks
of proteins are called amino acids.
Amino acids contain an ammonia group (amino) as well as a carboxyl
group (acid). Example amino acids include alanine, glycine, lysine,
glutamic acid, arginine.

Anaphase - fourth part of the
cell cycle during which chromosomes
are pulled toward the poles of the cell.

Antibodies - proteins (four
chains) produced by lymphocytes having
a very distinctive shape that enables them to bind tightly to
molecules that "fit" into the shape (like a lock fits
a key). The molecule bound by an antibody is referred to as an
antigen.

Dideoxynucleotide - a nucleotide
lacking an oxygen at both positions two and three of the sugar
ring. See figure.

Diploid - Cells containing two
complete sets of chromosomes. Most
of the cells of our body are diploid. The germ cells are haploid.

DNA - An acronym for deoxyribonucleic
acid. DNA is the genetic material, or "blueprint" of
the cell. Chromosomes contain DNA
(proteins too). DNA carries information
to make all of the proteins of a cell. DNA is composed of two
chains of polynucleotides intertwined with each other (figure)
in a very specific way. Each polynucleotide chain contains sufficient
information to replicate the other
strand under proper conditions.

Enhancer - a eukaryotic DNA sequence that can affect the transcription of a gene.
Enhancers are different from promoters
in their ability to be located long distances away from the gene
(over 1000 nucleotides, in some cases)
and their location - upstream or downstream
of a gene.

Expression vector - for our
purposes, we will define an expression vector as a plasmid
containing an E. coli replication origin,
a selectable marker (such as antibiotic resistance), and an E.
coli promoter upstream of the region
where the protein coding sequence
is placed.

Gel electrophoresis - laboratory
process for separating macromolecules on the basis of size.

Gene - The fundamental unit
of inheritance. A part of the cellular "blueprint" which
provides the necessary information for making a protein.
(Note - biotechnologists also use the term gene in a broader sense
to include the parts of DNA that are transcribed into rRNA
and tRNA as well.) The cellular blueprint,
of course, is DNA.

Genetic Code - the "language"
of heredity. The genetic code defines sequence of nucleotides
in DNA which ultimately (via mRNA)
specifies a sequence of amino acids
in a protein. The "letters"
of the language are referred to as codons.
Proteins in such a scheme may be thought to be "words"
(that is - composed of a specific sequence of letters). (See Figure). Though there are slight variations
of the genetic code that have been found, we think of the code
as being "universal" - that is, the same from one organism
to another.

Genetic Material - The "blueprint"
for all of the proteins needed for a cell. DNA
is the genetic material in all cells and most viruses. DNA
is a component of chromosomes.

Haploid - cells
containing only a single set of chromosomes.
Our germ cells are haploid. The rest of our cells are diploid.

Heterozygous - word used to
describe the situation where an individual has genes
for different traits (such as brown and blue eyes) at the same
chromosomal locus of their paired chromosomes.
Opposite of homozygous.

Histones - Small positively
charged proteins that interact with DNA
non-specifically. The structures they form in complex with DNA (DNA is "rolled" around
the histones) are referred to as nucleosomes, and the effect of
their wrapping in this manner is to reduce the effective length
of DNA in the cell. See
Picture.

Homozygous - word used to describe
the situation where an individual has the same gene
coding for the same trait (such as brown and brown eyes) at the
same place on a chromosomal pair.
Opposite of heterozygous.

Labeling - to attach a an identifying
marker of some sort to a nucleic acid
or protein. Usually the marker is
a radioactive element, such as 32P, but non-radioactive markers
are also available.

Lagging Strand Synthesis - In
DNA synthesis, polymerization occurs
both in the direction of the nearest replication
fork and away from it. Polymerization away from the nearest
replication fork occurs with fits and starts and is referred to
as lagging strand synthesis. The short fragments produced in lagging
strand synthesis are called Okazaki fragments.
(See also leading strand synthesis
and figure).

Leading Strand Synthesis - In
DNA synthesis, polymerization occurs both in the direction of
the nearest replication fork
and away from it. Polymerization towards the nearest replication
fork is called leading strand synthesis and produces newly synthesized
segments of DNA longer than those produced in lagging
strand synthesis. (See figure).

Library - A collection of all
the sequences of an organism (genomic
library) or its genes (cDNA library).
Though a solution of genomic DNA would
technically be a library by this definition, the term is usually
applied only when the sequences are all contained in (ligated
to) a cloning vector (plasmid).

Lipid Bilayer - A double layer
of phospholipids serving as the boundary between the cell
and its environment. The phospholipids are oriented such that
the "polar" portion (containing phosphate) is oriented
outwards and the non-polar portion is oriented inwards.

Locus - term used to describe
a specific site on a chromosome. We
speak of a gene as being located at
a specific chromosomal locus.

Macromolecule - large molecules
of a cell are called macromolecules. Typically they are a polymer
(molecule containing hundreds, thousands, or millions of common
building block molecules linked end-to-end). The individual building
blocks of a polymer are called monomers.
Starch is a polymer of units of the sugar glucose. Proteins
are macromolecules that are polymers of amino
acids. DNA and RNA
are polymers of nucleotide units.
The sequence with which the amino acids
of a protein are linked together
give the protein its characteristic activity. The sequence of
the nucleotides in DNA and RNA ultimately determines the sequence
of the amino acids in a protein.

Meiosis - A type of cell division
in which cells divide without replication
of the chromosomes. Consequently,
diploid cells (2 complete sets of
chromosomes) become haploid (1 complete
set of chromosomes). Gametes (sperm and egg) go through meiosis.
Upon fertilization, the fertilized egg contains two complete sets
of chromosomes and is diploid.

Metaphase - third part of the
mitotic cycle in which the chromosomes
are aligned at the metaphase plate in preparation for anaphase.

Mitosis - a term used generally
to refer to the process of cell division.
Technically the term is used to describe the division of the nucleus. Chromosomes
are duplicated during mitosis and the cell
divides in half, each half obtaining a complete set (copy) of
the chromosome(s). The pair of cells produced by mitosis are called
daughter cells.

Monomer - individual unit of
a polymer. For examply, AMP is a monomer of RNA,
which is a polymer of nucleotides.

Mutation - any alteration of
the sequence of nucleotides in a DNA molecule is described as a mutation.
Since the sequence of nucleotides
in a DNA may specify the sequence of amino
acids in a protein, mutations
in DNA can give rise to mutant proteins, which may have aberrant
(often undesired) activities from their unmutated forms.

Nucleic Acids - a term is used
to refer to DNA and RNA
in general. Technically the term refers to a polymer of nucleotides.

Nucleoside - a base linked to
a sugar. The difference between a nucleotide
and a nucleoside is that a nucleotide is a base plus a sugar plus
one or more phosphates. A nucleoside has no phosphate. Please
note that the base names are changed when they are linked to a
sugar. Guanine becomes guanosine. Adenine becomes adenosine. Thymine
becomes thymidine. Cytosine becomes
cytidine. Uracil becomes uridine.

Origin of Replication - a site
within a chromosome at which DNA replication
events begin. Origins have specific DNA
sequences that are recognized by the proteins
involved in initiating replication. E. coli has a single replication
origin on its circular chromosome called oriC.
Binding of dnaA protein is an important
first step in initiation of E. coli replication. Replication proceeds
in both directions (bidirectionally) from oriC.

PCR - an acronym for the Polymerase
Chain Reaction, a technique for specifically amplifying a desired
sequence apart from all the other sequences surrounding it.

Peptide bonds - the fundamental
covalent linkage between adjacent amino
acids in a protein. Peptide bonds
are formed by the joining of the carboxyl group of one amino acid
to the alpha amino group of another amino acid.

Phenotype - the physical characteristics
of a cell or an organism that arise from its genetic make-up (genotype). For example, blond hair is
a phentoype.

PlasmaMembrane - The
outer boundary of an animal cell
is a plasma membrane. Membranes protect the cell from the outside
environment. Membranes are composed of lipid
bilayers. Plant cells have a
rigid cell wall outside of the plasma membrane.

Plasmid - A piece of DNA
capable of replicating independently of the chromosomal DNA. Plasmids
must contain a replication origin.
Numerous plasmids (both linear and circular) from many species
are known. Most commonly the plasmids employed by biotechnologists
are small (under 7,000 base pairs), circular ones capable of replicating
in E. coli.

Ploidy - word used to describe
the number of copies of the chromosomes
a cell contains. Cells in multicellular organisms are often diploid - they have two complete sets
of chromosomes. Human cells have 23 pairs (that is, 2 complete
sets of 23) of chromosomes. Haploid
cells contain only a single copy of the chromosome(s). Gametes
(sperm and egg cells) are haploid because they have gone through
meiosis.

Poly-A tail - sequence of about
100 nucleotides of A at the 3' end
of eukaryotic mRNAs. The signal for
the tail is the sequence AAUAAA approximately 11-30 nucleotides
5' to the poly-A site. Poly-A tails appear to play a role in stability
of mRNAs. Though the majority of eukaryotic
mRNAs get a poly-A tail, not all do.

Primer - an essential template
requirement for DNA polymerases.
Consists of an oligonucleotide hybridized to a duplex DNA. The
oligonucleotide must have a free 3' end from which DNA polymerase
initiates replication. Primers are very useful for
defining sites of initiating DNA replication
for processes such as the Polymerase Chain Reaction (PCR). (See
RNA Primer).

Probe - a radioactively labeled
fragment of nucleic acid (usually DNA)
of a desired sequence. Probes can be used in blotting techniques
to identify desired sequences by the fact that they are complementary
to them.

Processivity - a term used
to describe the tendency of an enzyme to act on DNA
without falling off. The more processive an enzyme is, the longer
it will act on DNA before falling off. Subunit
Beta helps the DNA Pol III
holoenzyme to be more processive.

Prokaryotic cells - single cell life forms lacking a nucleus. Often
thought of as primitive. Prokaryotic cells are generally much
smaller than eukaryotic cells. Bacteria
are prokaryotes.

Prophase - First part of the
cycle of mitosis during which the
chromosomes become apparent. Prior
to this they are not very visible.

Prometaphase - Second part of
the mitotic cycle during which the
nucleus has dissolved, and the paired
sister chromatids become linked to spindle fibers.

Proteins - macromolecules
composed of polymer(s) of amino acids
that perform the "work" of a cell.
Some proteins function as enzymes
and catalyze the chemical reactions
in a cell. Other proteins provide structural integrity to the
cell. Still others exert their effects by "turning on"
or "turning off" the synthesis of other proteins. The
amino acids in a protein are linked together by what are called
"peptide bonds". Proteins
are often called peptides or polypeptides.

Proto-oncogene - cellular gene
that, when mutated, can cause a cell to become cancerous. See
oncogene.

Recombination - In nature, a
process whereby DNA sequences
in chromosomes are rearranged. (In
the laboratory, scientists cause recombination with restriction
enzymes and DNA ligase). Recombination in nature usually involves
migration of a DNA sequence from one site on a chromosome to another
where a similar sequence resides. Such a recombination is referred
to as homologous recombination.

Restriction enzyme - an enzyme
often employed in biotechnology. It acts to cleave DNA
at a specific sequence called a recognition site. EcoRI is one
such restriction enzyme.

Restriction map - a circular
or linear "map" for a DNA
showing the location of restriction enzyme recognition sites on
it. Restriction maps are assembled using information from multiple
cuts of DNA with different enzymes. The size of the DNA fragments
from such cuts are analyzed by gel electrophoresis,
and the location of sites in the parental DNA are inferred by
comparing the pattern generated by cutting with a single enzyme
compared to cutting it with pairs of enzymes.

Retrovirus - a relatively small
RNA virus that typically codes for
at least three common genes (called GAG, POL, and ENV). The POL
gene is a reverse transcriptase that
enables the viral RNA to be converted to DNA
upon infection of a cell. The DNA can invade the cell's chromosomes
and produce many copies of more viral RNA. HIV is a retrovirus.

Reverse Transcriptase - an enzyme
that can use RNA as a template and
can make DNA in the presence
of dNTPs.

RFLPs - an acronym for Restriction
Fragment Length Polymorphisms. RFLPs refer to different sizes
of restriction fragments in the same
area of the genome in two different DNAs.
RFLPs are evidence of mutation/modification
of DNA sequence occurring at a particular site of a chromosome.

Ribonucleotides - the fundamental
building blocks of RNA. The four ribonucleotides
found in RNA are abbreviated AMP, GMP, CMP, and UMP. Ribonucleotides
differ from deoxyribonucleotides
in the usage of the base U instead of T and in the use of ribose
as the sugar instead of deoxyribose. See also nucleotides.

Ribozyme - an RNA
that can catalyze a reaction. The
first known ribozymes were the self-splicing RNAs.

RNA - an acronym for RiboNucleic
Acid, a type of nucleic acid related
to DNA and which is made from DNA
in a process called transcription.
RNA is a polymer of ribonucleotides,
which are so named because they contain the sugar ribose.
Primary RNAs in the cell include transfer RNA (tRNA),
messenger RNA (mRNA), and ribosomal
RNA (rRNA).

snRNAs - an acronym for small
nuclear RNAs, snRNAs are components of snRNPs - ribonucleic acid-protein
complexes involved in splicing RNAs
in the nucleus of eukaryotic
cells. snRNAs include U1, U2, U5, and U4/U6.

snRNPs - a complex of (usually)
a single snRNA and several (about
10) nuclear proteins. snRNPs bind to the RNA
that is to be spliced and catalyze
the excision of the introns and covalent
joining of the exons. The resulting
intron structure from this reaction is in the form of a lariat.
snRNPs are named for the snRNA(s) they contain.

Supercoiling - word used to
describe alterations of a DNA helix
that underwind (negative supercoiling) or overwind (positive supercoiling)
the most relaxed form of the DNA. See topoisomerases.

TATA Box - a region rich in
the sequence A-T found about 25 base pairs before the startpoint
of eukaryotictranscription
start point or about 10 base pairs before the startpoint of a
prokaryotic transcription start point.

Telomere - structure found a
t the end of a eukaryotic chromosome.
Has a distinct repetitious sequence within the DNA.

Telophase - fifth part of the
cell cycle during which chromosomes
reach the poles of a cell.

Translation - The process by
which information in DNA is ultimately
converted to make a protein. Information
is initially passed from DNA to mRNA.
Ribosomes "read" the sequence
of bases in mRNA and sequentially attach amino
acids (via peptide bonds) corresponding
to what they read.

Transposon - a "mobile
genetic element". Transposons are pieces of DNA
that are capable of moving from one chromosomal location to another,
or from a chromosome in one cell to
a chromosome in another cell.

tRNA - transfer RNA. Small RNA molecules containing an anti-codon
loop at one end (for pairing with codons
during translation) and an amino
acid covalently linked to the 3' end of the strand at the
other end. Amino acids are specific to the anti-codon on the tRNA.

Upstream - molecular biology
lingo meaning 5' to a defined point. The initiation site of transcription might be described as upstream
of the termination site. See downstream.

Wild Type - DNAs
that have been mutated are described
as mutated or mutant. Unmutated DNAs are called wild type. The
terms wild type and mutant are also used to describe proteins
or cells resulting from these mutations.